Recent genome sequencing efforts, which have revealed that our current discovery methods access, at best, 10% of the small molecule repertoire of bacteria. A detailed analysis of the sequenced genomes of actinomycetes, the group of bacteria responsible for over 50% of all antibiotics, has demonstrated that the great majority of biosynthetic gene clusters, the sets of genes responsible for production of bioactive compounds, remain inactive or ‘silent’ for unknown reasons. Given the track record of natural products as therapeutics, these clusters, dubbed silent or cryptic gene clusters, harbor an extensive supply of potential drug candidates, and successful approaches that systematically awaken them would have a profound impact on drug discovery.
The problem of silent gene clusters is challenging because an unknown signal activates an uncharacterized gene cluster leading to the production of a new metabolite. There are three variables in this process, two of which can be determined experimentally or computationally: bioinformatic methods allow for facile identification of genes that generate nonribosomal peptides, polyketides, and terpenes, and pinpointing gene assemblies of novel metabolites within these families can be performed with good fidelity. Once activated, the product of the gene cluster can be experimentally identified by differential metabolomics facilitating its isolation and structural elucidation via multi-dimensional NMR. Thus, the problem of crypticity may be reduced to the large variety of signals that may act as elicitors or activators of silent clusters.
Thus far, no method has been described that allows for identification of elicitors of a given silent gene cluster. An efficient platform that enables discovery of small molecule activators would allow scrutiny of the regulatory pathways that lead to induction of silent biosynthetic clusters as well as structural and functional elucidation of their products.